You can specify your reference genome with "-reference" option. The
reference file should be formatted in fasta, and multiple files can be specified like
"-reference chr1.fa chr2.fa". You can also use a wildcard for specifying multiple files
as "-reference chr*.fa".

The options "-species"and "-revision" specify the name
of species and revision of genome sequences, respectively. These options also specify the
directory names and the file name to store the index structure. In default settings, BMap
uses the "Revisions" directory, which is located in the same directory with the executable file, to store the index files.

In this step, BMap create suffix arrays for two duplicated reference genome
sequences; one is generated by converting every C to T (C2T) and the other is generated by converting every G to A (G2A). These suffix arrays are created using an algorithm termed "induced sorting"
(Ge Nong et al., 2011), which is able to build the index structure in linear computational
time with the length of input sequence. After creating the suffix arrays, BMap next
constructs a Burrows-Wheeler Transform (BWT) version of C2T and G2A sequences required to construct an FM-index (Ferragina P. & Manzini M., 2001).

2. Map your reads

After creation of the index file, you can do mapping with BMap. BMap accept fasta, fastq
and illumina qseq file as query file(s) for single-end reads. Only pair(s) of fastq files
are acceptable for paired-end reads. The simplest commands for single-end and paired-end reads
are as follows.

1. Specifying reference genome or index file

Specify path to index file. Mutually exclusive with the combination of options "-species" and "-revision"

-root_dir

string

Specify the path to root for index path tree. (default="Revisions")

-binseq

string

Specify path to binseq file

2. Specifying number of threads used for mapping

Option

Value type

Descriptions

-thread

integer

Specify number of CPU core or threads used in mapping mode. (default=1)

3. Controlling sensitivity and speed of mapping

Option

Value type

Descriptions

-seedoffset

integer

Specify offset position of read to take first seed (default=1)

-seedstep

integer

Specify step width of seed (default=1)

-seediterate

integer

Specify number of repeat to take seeds (default=100)

-minseedlen

integer

Specify minimum length of seed (default=16)

-maxseedlen

integer

Specify maximum length of seed (default=26)

-minseedcount

integer

Specify minimum seed count for a candidate genomic region to be considered
for verification of alignment with read.

-maxseedcount

integer

Specify maximum seed count to be considered for verification of alignment with read.

4. Controlling stringency of alignment

Option

Value type

Descriptions

-minscore

integer

Specify minimum score for alignment to report. Value for a match and
a mismatch are 5 point and -30 point, respectively. A mismatch between C on reference
and T on reads is considered as a match. (default=150)

5. Selection of type of index structure and memory usage

Option

Value type

Descriptions

-bwt

integer

Specify index structure dependent on values:

0: Use suffix array.

1: Use FM-index with -SCF 4 -SCL 16

2: Use FM-index with -SCF 8 -SCL 16

3: Use FM-index with -SCF 16 -SCL 16

4: Use FM-index with -SCF 32 -SCL 32

5: Use FM-index with -SCF 64 -SCL 64

6: Use FM-index with -SCF 128 -SCL 128

6. Manipulating I/O

Option

Value type

Descriptions

-reference

string(s)

Specify input file name(s) for creating index

-fasta

string

Specify input file formatted in fasta. Only available
for single-end sequencing reads

-fastq

string(s)

Specify input file formatted in fastq. Only available
for single-end sequencing reads

-qseq

string(s)

Specify input file formatted in qseq. Only available
for single-end sequencing reads